3.1 Loading a LiPD file

library(lipdR)
library(geoChronR)

## Registered S3 method overwritten by 'spatstat.geom':
##   method     from
##   print.boxx cli

## Welcome to geoChronR version 1.1.0!

##

## 
## Attaching package: 'geoChronR'

## The following objects are masked from 'package:lipdR':
## 
##     createTSid, pullTsVariable

L <- readLipd("https://lipdverse.org/Temp12k/current_version/GEOFAR_KF16_MgCa.Repschlager.2016.lpd")

## [1] "reading: GEOFAR_KF16_MgCa.Repschlager.2016.lpd"

3.1a+b load it from URL and from computer

L <- readLipd("https://lipdverse.org/Temp12k/current_version/MD01_2378.Xu.2008.lpd")

## [1] "reading: MD01_2378.Xu.2008.lpd"

#from computer: L <- readLipd()

Plot

summary_plot <- plotSummary(L,
                            paleo.data.var = "temperature",
                            chron.age.var = "age",
                            chron.depth.var = "depth_bottom",
                            chron.age.14c.var = NULL)

## [1] "Found it! Moving on..."
## [1] "Found it! Moving on..."
## [1] "Found it! Moving on..."
## [1] "Found it! Moving on..."

temp <- selectData(L,paleo.or.chron = "paleoData", var.name = 'temperature',
                   table.type = "meas",meas.table.num = 1)

## [1] "Found it! Moving on..."

c14 <- selectData(L,paleo.or.chron = "chronData", var.name = 'c14_date')

## [1] "Found it! Moving on..."

3.2

eur <- readLipd("https://lipdverse.org/geoChronR-examples/euro/Euro2k.zip")

## [1] "reading: Arc-AkademiiNaukIceCap.Opel.2013.lpd"
## [1] "reading: Arc-Forfjorddalen.McCarroll.2013.lpd"
## [1] "reading: Arc-GulfofAlaska.Wilson.2014.lpd"
## [1] "reading: Arc-Indigirka.Hughes.1999.lpd"
## [1] "reading: Arc-Jamtland.Wilson.2016.lpd"
## [1] "reading: Arc-Kittelfjall.Bjorklund.2012.lpd"
## [1] "reading: Arc-PolarUrals.Wilson.2015.lpd"
## [1] "reading: Arc-Tjeggelvas.Bjorklund.2012.lpd"
## [1] "reading: Arc-Tornetrask.Melvin.2012.lpd"
## [1] "reading: Eur-CentralandEasternPyrenees.Pla.2004.lpd"
## [1] "reading: Eur-CentralEurope.Dobrovoln.2009.lpd"
## [1] "reading: Eur-CoastofPortugal.Abrantes.2011.lpd"
## [1] "reading: Eur-EasternCarpathianMountains.Popa.2008.lpd"
## [1] "reading: Eur-EuropeanAlps.Bntgen.2011.lpd"
## [1] "reading: Eur-FinnishLakelands.Helama.2014.lpd"
## [1] "reading: Eur-LakeSilvaplana.Larocque-Tobler.2010.lpd"
## [1] "reading: Eur-LakeSilvaplana.Trachsel.2010.lpd"
## [1] "reading: Eur-Ltschental.Bntgen.2006.lpd"
## [1] "reading: Eur-MaritimeFrenchAlps.Bntgen.2012.lpd"
## [1] "reading: Eur-NorthernScandinavia.Esper.2012.lpd"
## [1] "reading: Eur-NorthernSpain.Martn-Chivelet.2011.lpd"
## [1] "reading: Eur-RAPiD-17-5P.Moffa-Sanchez.2014.lpd"
## [1] "reading: Eur-Seebergsee.Larocque-Tobler.2012.lpd"
## [1] "reading: Eur-SpanishPyrenees.Dorado-Linan.2012.lpd"
## [1] "reading: Eur-SpannagelCave.Mangini.2005.lpd"
## [1] "reading: Eur-Stockholm.Leijonhufvud.2009.lpd"
## [1] "reading: Eur-Tallinn.Tarand.2001.lpd"
## [1] "reading: Eur-TatraMountains.Bntgen.2013.lpd"
## [1] "reading: Ocn-AqabaJordanAQ18.Heiss.1999.lpd"
## [1] "reading: Ocn-AqabaJordanAQ19.Heiss.1999.lpd"
## [1] "reading: Ocn-RedSea.Felis.2000.lpd"

mapLipd(eur,projection = "mollweide",global = TRUE)

TS <- extractTs(eur)
summ <- plotSummaryTs(TS,age.var = "year",
                      sort.var = "geo_pages2kRegion")

3.2.1

library(dplyr)

## 
## Attaching package: 'dplyr'

## The following objects are masked from 'package:stats':
## 
##     filter, lag

## The following objects are masked from 'package:base':
## 
##     intersect, setdiff, setequal, union

ts.tib <- ts2tibble(TS)
filtered.tib <- ts.tib %>% 
   filter(between(geo_latitude,30,80) & between(geo_longitude,-30,60)) %>%
   filter(archiveType == "tree") %>% 
   filter(paleoData_useInGlobalTemperatureAnalysis == TRUE)

nTS <- as.lipdTs(filtered.tib) #convert it back (for now)
plotSummaryTs(nTS,age.var = "year",f = .1)

## TableGrob (5 x 3) "arrange": 2 grobs
##   z     cells    name           grob
## 1 1 (1-3,1-3) arrange gtable[layout]
## 2 2 (4-5,1-3) arrange gtable[layout]

Invert.var points a variable which can flip the timeseries: in this case invert.var = ‘interpretation1_interpDirection’?

longTib <- as.lipdTsTibbleLong(filtered.tib) %>% 
   dplyr::filter(between(year,1000,2000))

## creating a lipdTsTibbleLong using year as the age.var

#devtools::install_github("ropenscilabs/ochRe")
library(ochRe)
ramp <- function(nColors){
  pal <- colorRampPalette(ochre_palettes[["lorikeet"]])
  pal(nColors)
  }

plotTimeseriesStack(longTib,color.var = "paleoData_proxy",
                    line.size = 0.2,
                    color.ramp = ramp,
                    invert.var = 'interpretation1_interpDirection')

ramp2 <- function(nColors){
  pal <- colorRampPalette(ochre_palettes[["namatjira_div"]])
  pal(nColors)
}

longTib %>% 
  filter(paleoData_proxy =='MXD') %>% 
  plotTimeseriesStack(color.var = "geo_pages2kRegion",
                    line.size = 0.2,
                    color.ramp = ramp2,
                    invert.var = 'interpretation1_interpDirection')

Exercise 1

3.1 Loading a LiPD file

Plot

3.2

3.2.1